Electronic structures and chemical bonding in 4d transition metal monohalides

Bond distances, vibrational frequencies, dipole moments, dissociation energies, electron affinities, and ionization potentials of NIX (XM = Y-Cd, X = F, Cl, Br, I) molecules in neutral, positively, and negatively charged ions were studied by density functional method, B3LYP. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides ionic component, covalent bonds are formed between the 4d transition metal s, d orbitals, and the p orbital of halogen. For both neutral and charged molecules, the fluorides have the shortest bond distance, iodides the longest. Although the opposite situation is observed for vibrational frequency, that is, fluorides have the largest value, iodides the smallest. For neutral and anionic species, the dissociation energy tends to decrease with the increasing atomic number from Y to Cd, suggesting the decreasing or weakening of the bond strength. For cationic species, the trend is observed from Y to Ag.

Interaction of H-2 with transition metal homonuclear dimers Cu-2, Ag-2, Au-2 and heteronuclear dimers PdCu, PdAg and PdAu

The reaction mechanisms of the H-2 with the homonuclear dimers M-2 (Cu, Ag, Au) and the heteronuclear dimers PdM (M = Cu, Ag, Au) were studied by use of density functional theory. For the H-2 reactions with homonuclear dimers M-2 (Cu, Ag, Au), it was found that it is easier for Au-2 to dissociate the hydrogen molecule compared with Cu-2 and Ag-2. For H-2 reactions with the heteronuclear dimers PdM (M = Cu, Ag, An), the hydrogen molecule can be easily dissociated at Pd site, rather than at noble metal site.

Electronic structures of 4d transition metal monoxides by density functional theory

Bond distances, dissociation energies, ionization potentials and electron affinities of 4d transition metal monoxides from YO to CdO and their positive and negative ions were studied by use of density functional methods B3LYP, BLYP, B3PW91, BPW91, B3P86, BP86, SVWN, MPW1PW91 and PBE1PBE. It was found that calculated properties are highly dependent on the functionals employed, especially for dissociation energy. For most neutral species, pure density functionals BLYP, BPW91 and BP86 have good performance in predicting dissociation energy than hybrid density functionals B3LYP, B3PW91 and B3P86. In addition, BLYP gives the largest bond distance compared with other density functional methods, while SVWN gives shortest bond distance, largest dissociation energy and electron affinity. For the ground state, the spin multiplicity of the charged species can be obtained by +/- 1 of their corresponding neutral species.

Electronic structures of 5d transition metal monoxides by density functional theory

Bond distances, vibrational frequencies, electron affinities, ionization potentials, and dissociation energies of the diatomic 5d transition metal (except La) monoxides and their positively and negatively charged ions were studied by use of density functional methods B3LYP, BLYP, B3PW91, BPW91, B3P86, BP86, MPW1PW91, PBE1PBE, and SVWN. Our calculation shows that for each individual species, the calculated properties are quite sensitive to the method used. Compared with hybrid density functional method B3PW91 (B3P86), pure density functional method BPW91 (BP86) gives longer bond distance (lower vibrational frequency) from HfO to PtO for neutral species, HfO+ to IrO+ for cationic species, and HfO- to AuO- for anionic species. While for B3LYP and BLYP, the trend was observed for cationic species from HfO+ to IrO+ and anionic species from HfO- to AuO- (except TaO-), but not for neutrals. Pure density function methods BLYP, BPW91, and BP86 give larger dissociation energy compared with hybrid density functional methods B3LYP, B3PW91, and B3P86. SVWN in most cases gives the smallest bond distance, while BLYP gives the largest value. MPW1PW91 and PBE1PBE show the same performance in predicting the spectroscopic constants.

Theoretical investigation of 5D-metal monocarbide

Bond distances, vibrational frequencies, electron affinities, ionization potentials and dissociation energies of the title molecules in neutral, positively and negatively charged ions were studied by use of density functional method. The calculated results were compared with previous theoretical and experimental studies. Ground states for each molecule were assigned. It was found that for some molecules, low-lying state, in which the energy is much close to the ground state, was obtained. In this case, further studies both experimentally and theoretically are necessary in order to find the true global minimum.

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion.Including the configurational dependence will challenge the transition state theory of protein folding.

Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

Trends in elasticity and electronic structure of 5d transition metal diborides: first-principles calculations

We investigate the cohesive energy, heat of formation, elastic constant and electronic band structure of transition metal diborides TMB2 (TM = Hf, Ta, W, Re, Os and Ir, Pt) in the Pmmn space group using the ab initio pseudopotential total energy method. Our calculations indicate that there is a relationship between elastic constant and valence electron concentration (VEC): the bulk modulus and shear modulus achieve their maximum when the VEC is in the range of 6.8-7.2. In addition, trends in the elastic constant are well explained in terms of electronic band structure analysis, e.g., occupation of valence electrons in states near the Fermi level, which determines the cohesive energy and elastic properties. The maximum in bulk modulus and shear modulus is attributed to the nearly complete filling of TM d-B p bonding states without filling the antibonding states. On the basis of the observed relationship, we predict that alloying W and Re in the orthorhombic structure OsB2 might be harder than alloying the Ir element. Indeed, the further calculations confirmed this expectation.

Density functional study of the second row transition metal dimers

Equilibrium geometries, vibrational frequencies and dissociation energies of the second row transition metal dimers (from Y-2 to Cd-2 except Tc-2) ere studied by use of density functional methods B3LYP, BLYP, B3PW91, BHLYP, BP86, B3P86, SVWN, MPW1PW91 and PBE1PBE. The accuracy DFT methods is found to be highly dependent on the functional employed, in particular for vibrational frequency and dissociation energy. In most cases, the predicted bond distance is in general agreement with experiment and previous theoretical results. For van der Waals dimer Cd-2, B3LYP and BLYP have excellent performance in predicting the bond distance. For Ag-2, all density functional methods used in this study perform well in producing the bond distance, vibrational frequency and dissociation energy.

Structural stability and electronic state of transition metal trimers

Ground state geometries were searched for transition metal trimers Sc-3, Y-3, La-3, Lu-3, Ti-3, Zr-3, and Hf-3 by density functional methods. For all the studied trimers, our calculation indicates that the ground state geometries are either equilateral triangle (Zr-3 and Hf-3) or near equilateral triangle (Ti-3, Sc-3, Y-3, La-3, and Lu-3). For rare earth trimers Sc-3, Y-3, La-3, and Lu-3, isosceles triangle (near equilateral triangle) at quartet state is the ground state. Isosceles triangle at doublet state is the competitive candidate for the ground state. For Zr-3 and Hf-3, equilateral triangle at singlet state is the most stable. For Ti-3, isosceles triangle (near equilateral triangle) at quintet state gives the ground state. For Sc-3, Zr-3, and Hf-3, where experimental results are available, the predicted geometries are in agreement with experiment in which the ground state is equilateral triangle (Zr-3) or fluxional (Sc-3 and Hf-3). For Y-3, the calculated geometry is in agreement with experimental observation and previous theoretical study that Y-3 is a bent molecule for the ground state.

Brittle-ductile transition of polypropylene/ethyllene-propylene-diene monomer blends induced by size, temperature, and time

To study the brittle-ductile transition (BDT) of polypropylene (PP)/ethylene-propylene-diene monomer (EPDM) blends induced by size, temperature, and time, the toughness of the PP/EPDM blends was investigated over wide ranges of EPDM content, temperature, and strain rate. The toughness of the blends was determined from the tensile fracture energy of the side-edge notched samples. The concept of interparticle distance (ID) was introduced into this study to probe the size effect on the BDT of PP/EPDM blends, whereas the effect of time corresponded to that of strain rate. The BDT induced by size, temperature, and time was observed in the fracture energy versus ID, temperature, and strain rate. The critical BDT temperatures for various EPDM contents at different initial strain rates were obtained from these transitions. The critical interparticle distance (IDc) increased nonlinearly with increasing temperature, and when the initial strain rate was lower, the IDc was larger. Moreover, the variation of the reciprocal of the initial strain rate with the reciprocal of temperature followed different straight lines for various EPDM contents. These straight lines were with the same slope.

Dominant kinetic paths on biomolecular binding-folding energy landscape

The identification of kinetic pathways is a central issue in understanding the nature of flexible binding. A new approach is proposed here to study the dynamics of this binding-folding process through the establishment of a path integral framework on the underlying energy landscape. The dominant kinetic paths of binding and folding can be determined and quantified. In this case, the corresponding kinetic paths of binding are shown to be intimately correlated with those of folding and the dynamics becomes quite cooperative. The kinetic time can be obtained through the contributions from the dominant paths and has a U-shape dependence on temperature.

Geometries and electronic properties of Ta-n, TanO and TaOn (n=1-3) clusters

Geometries, vibrational frequencies, electron affinities, ionization potentials and dissociation energies of the title clusters in both neutral and positively and negatively charged states were studied by use of density functional theory. For both neutral and charged species, different initial isomers were studied in order to determine the structure with the lowest energy. Vibrational analysis was also performed in order to characterize these isomers. For Ta-2, Ta-Ta metallic bond is strengthened by adding or removing an electron, i.e. the charged species are much more stable than the neutral counterpart. For Ta-3, equilateral triangle with D-3h symmetry has the lowest energy for both neutral and charged species (near equilateral triangle for cation). TaO and its charged species have much larger dissociation energy compared with other tantalum oxides. For Ta2O and TaO2. structure with C-2v symmetry is much more stable than linear chains. For Ta3O, planar structure with doubly bridging oxygen atoms of C-2v, symmetry is the global minimum for both neutral and charged species. While for TaO3, three-dimensional structures are favored for both neutral (C-1 symmetry) and charged species (C-3v symmetry).

Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding

We study the nature of biomolecular binding. We found that in general there exists several thermodynamic phases: a native binding phase, a non-native phase, and a glass or local trapping phase. The quantitative optimal criterion for the binding specificity is found to be the maximization of the ratio of the binding transition temperature versus the trapping transition temperature, or equivalently the ratio of the energy gap of binding between the native state and the average non-native states versus the dispersion or variance of the non-native states. This leads to a funneled binding energy landscape.

Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We found that the first passage-time (FPT) distribution undergoes a dynamic transition at a temperature below which the FPT distribution develops a power-law tail, a signature of the intermittent nonexponential kinetic phenomena for the folding dynamics. Possible applications to single-molecule dynamics experiments are discussed.